The authentic Hubei Chinese medicinal and edible herb Fubaiju, Chrysanthemum morifolium, is rich in flavonoids. An evaluation method based on an in vitro chemical antioxidant assay and an in vivo C. elegans model was proposed to investigate the antioxidant capacities of flavone compounds, using the free-radical-scavenging rate, antioxidant enzyme activity, and nematode fluorescence intensity as indicators. The common peaks indicated in the spectral fingerprints of flavonoids from 15 different brands of Fubaiju Chrysanthemum were assessed to investigate the spectrum-effect relationship between Fubaiju Chrysanthemum flavonoids and their antioxidant activities. The maximum DPPH and the ABTS+ free-radical-scavenging rates of the flavonoid extract of Fubaiju were 83.14% and 75.32%, respectively. Moreover, the flavonoid extract significantly improved the antioxidant enzyme activity in nematodes and enhanced their oxidative stress resistance. Eight characteristic common peaks in the flavonoid spectral fingerprint profile all showed a certain correlation with antioxidant activity, especially peak 3, which had the most significant correlation and may represent luteolin-7-O-β-Dglucoside. Peak 4 showed the most significant correlation with ABTS+ free-radical scavenging and may represent luteolin-7-O-β-D-glucuronide. The flavonoid extract from Fubaiju Chrysanthemum exhibited promising antioxidant activity, providing a reference for the subsequent derivation and development of antioxidants.